Int. J. Life. Sci. Scienti. Res., VOL 2, ISSUE 2, pp: 102-109
(ISSN: 2455-1716)
Impact Factor 2.4
MARCH-2016
Research Article (Open access)
Isolation, Screening and Characterisation of Polyhydroxyalkanoate Producing Bacteria from Oil Contaminated Site Rameshwari, R1*, Meenakshisundaram, M2 1 2
Cauvery College For Women, Tiruchirapalli, T.N, India
Nehru Memorial College (Autonomous), Puthanampatti, India
ABSTRACT- The development of human civilization throughout history has led to growing disruption of the natural balance and the occurrence of different types of pollution. Environmental pollution with petroleum and petrochemical products has been recognized as significant and serious problem. Diesel engine oil, which is one of the major products of crude oil, constitutes a major source of pollution in our environment. Therefore diesel engine oil can enter into the environment through wrecks of oil tankers carrying diesel oil, cleaning of diesel tanks by merchants, war ships carrying diesel oil and motor mechanics. In present study the microorganisms utilising petrol and diesel oil as carbon source were isolated and investigation of their characteristics towards the production of polyhydroxyalkanoates (PHA), which is now a days well known as biodegradable polymer.
Key Words- Petrol and Diesel oil contamination, Bioremediation, Biodegradable bacterial polymer, Sudan Black B staining, 16sr RNA sequencing -------------------------------------------------IJLSSR-----------------------------------------------
INTRODUCTION Automobiles used (waste) oil contains oxidation products,
high volatile fractions, dissolution of water-soluble
sediments, water and metallic particles resulting from
fractions, photochemical oxidation, drill, emulsification,
machinery wears, used batteries, organic and inorganic
microbial degradation and sedimentation. The concentra-
1
chemicals used in oil additives and metals . Oil pollution
tion of hydrocarbon and non-hydrocarbon components in
occurs when oil is introduced into the environment directly
crude oil from different sources differ greatly2. The
or indirectly by men’s impacts resulting in unfavorable
contamination of the aquatic system with heavy metals has
change in such a way that safety and welfare of any living
been on the increase since the last century due to industrial
organisms is endangered. Crude oil if spilled into the water
activities. Heavy metals are taken up as cations. Among the
spreads over a wide area forming a slick and oil in water
heavy metals detected in WSF are Pb, Cu, Zn, Cd, Ni, Cr,
immediately begins to undergo a variety of physical,
and V 3. The extensive usage of petrochemical plastics due
chemical and biological changes including evaporation of
to their versatile properties especially durability is causing
*
severe problem in waste management affecting the
Address for Correspondence:
R. Rameshwari
aesthetic quality of cities, water bodies and natural areas.
Assistant Professor
The
Department of Biotechnology
concern in terms of the environment4. Biopolymers are one
Cauvery College For Women, Trichy–18, India Deepak
product that can help to overcome problems caused by
Prashar Received: 21 Jan 2016/Revised: 13 Feb 2016/Accepted: 26 Feb 2016
petrochemical polymers are generated from renewable
accumulation of plastic wastes has become a major
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Int. J. Life. Sci. Scienti. Res., VOL 2, ISSUE 2
natural sources and are often biodegradable and nontoxic5. The most extensively studied thermoplastic biopolymers are the polyhydroxyalkanoates (PHA) and polylactic acid LA)6. In the present study, was carried out physicochemical characterization of soils from auto-mechanic workshops at
6
from mechanic workshop Oil contaminated sediment sample from mechanic workshop
SS3
K.K.Nagar, Trichy (site 2)
Summer
different depths (0-15 cm; 15-30 cm, 30-45 cm), namely
Physiochemical analysis
pH, clay, silt, sand, total organic carbon (TOC), exchangea-
The physiochemical parameters, i.e., pH, electrical
ble cations, and equally examined the distribution of heavy
conductivity (EC) and total dissolved solids (TDS) were
metals such as Pb, Cr, Cu, Zn, Fe, Ni, and Cd.
measured using field kit (Thermo Orion 5-Star Ph
MATERIALS AND METHODS
Multi-Meter) on the site and the concentrations of soluble
Petroleum and Diesel oil contaminated water and sediment
cations and anions (Ca2+, Mg2+, Na+, K+, CO3−, HCO3−, Cl−
samples from various sources during post monsoon and
and SO42−) were determined
according to the standard
summer season as outlined in Table 1 and used for the
methods
physicochemical, Trace metal and bacteriological analysis
required for microbiological analysis, held on iceboxes and
and also used for the isolation of bacteria. The 2000 mL of
processed within 12 h of collection.
water samples were collected with a 2500 mL sterile
Trace Metal analysis
container in each location. Thesediment samples were
For heavy metal analysis, the one liter of oil polluted water
collected by sterile spatula and stored insterile plastic
was acidified immediately with concentrated nitric acid
7
8-11
. All samples were collected with precautions
bags .
(HNO3). For trace metal study, acidified test water samples
TABLE 1. Collection of samples from different sources
were filtered by Whatman No.1 filter paper and processed
for isolation of PHA Synthesizing bacteria
(APDC + MIBK) for metal analysis. The sediment samples
S. NO
SAMPLE TYPE
1
Oil contaminated water sample from mechanic workshop Oil contaminated water sample from mechanic workshop Oil contaminated water sample from mechanic workshop Oil contaminated sediment sample from mechanic workshop Oil contaminated sediment sample
2
3
4
5
SAMPLE CODE SW1
PLACE OF SAMPLING Woraiyur, Trichy (site 1)
COLLECTION TIME
Tennur, Trichy (site 3)
Summer
K.K.Nagar, Trichy (site 2)
Summer
Summer
were air-dried and smaller than (>) 63 μm in size were kept back in pre-cleaned properly. Thenceforth, the dried sediment samples were crushed by agate mortar and pestle. Both the samples were processed with an aqua-regia mixture (i.e. HCl: HNO3= 3:1) in Teflon bomb and were
SW2
incubated at 140 °C for 2-3 days after dried and sieved samples. After incubation, the reaction mixture was filtered with Whatman No.1 filter paper. The trace metals in the sea
SW3
water, sea sediment and crabsamples were determined by the atomic absorption spectrophotometry (GBC SensAA AAS, Australia) in flame mode12.
SS1
Woraiyur, Trichy (site 1)
Summer
Tennur, Trichy (site 3)
Summer
Isolation and Purification of Bacterial Strains 1 gm of oil contaminated soil sample was taken, serially diluted, plated on nutrient agar plates and incubated at
SS2
37°C for 24h to calculate the bacterial colonies13. By using the above method 1 ml of sago wastewater sample was
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Int. J. Life. Sci. Scienti. Res., VOL 2, ISSUE 2
taken for analysis and to calculate the bacterial colonies.
sequenced using the 518F/800R primers. Sequencing
After incubation all bacterial colonies were purified on
reactions were performed using a ABI PRISM® BigDyeTM
nutrient agar plates and subsequently analyzed for PHAs
Terminator Cycle Sequencing Kits with AmpliTaq® DNA
accumulation and confirmed by Nile blue A staining, gram
polymerase (FS enzyme) (Applied Biosystems). Amplified
reaction, motility, spores staining and biochemical tests.
DNA obtained from PCR was then sequenced by using
Nile Blue A Staining
aABI 3730xl sequencer (Applied Biosystems). The
Heat fixed bacterial smear was stained with 1% aqueous solution of Nile blue A at 55ºC for 10 min. The slide was washed with tap water to remove the excess stain and washed with 8% aqueous acetic acid for 1 min. The stained smear was again washed with tap water and blot dried. Prior to observation, the slide was remoistened with a drop of water and coverslip was placed on the smear14. The slides were viewed in fluorescence microscopy at a wavelength of 480 nm.
Morphological Characterisation The three potent PHA accumulating strains B5, B7 and B24 were examined for theircolony morphology, pigmentation fluorescence, cell shape and gram reaction as per thestandard procedures15.
Biochemical Characterisation Biochemical tests were carried out as per the method given by Cappuccino and Sherman (1992) with 24 hr old cultures.
sequence of 16s rRNA gene was compared with the 16s rRNA gene sequences available in the National Center for Biotechnolgy using
their
Information (NCBI) public databases by World
Wide
Web
and
the
BLAST
(Protein- Protein blast).
RESULTS AND DISCUSSION The physicochemical properties of petrol and diesel oil contaminated sediment and water samples in mechanic workshop for the season summer was given in Table 2. The development of human civilization throughout history has led to growing disruption of the natural balance and the occurrence of different types of pollution17. Changes in soil properties due to contamination with petroleum- derived substances can lead to water and oxygen deficits as well as shortage of available forms of nitrogen and phosphorus18-20. Studies have shown that PAHs can be carcinogenic and/or mutagenic in some circumstances and have been classified as priority pollutants21.
Molecular Characterisation The selected strain was identified by ABI 3730xl sequencer (Applied Biosystems). The 16S rRNA gene was selectively with the 16S rRNA gene universal primer.
Dna Extraction, Amplification And Sequencing Bacterial Genomic DNA was isolated using the Insta GeneTM Matrix Genomic DNA isolation kit. Extracted DNA was The 16s rRNA was amplified using bacterial universal primers for Bacillus sp. 27f forward primer and 1492R reverse primer. Amplified PCR product was
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Int. J. Life. Sci. Scienti. Res., VOL 2, ISSUE 2
Table 2. Physiochemical parameters in oil polluted area water and sediment samples in Tiruchirappalli, Tamil Nadu – Summer 2015 S. No.
Parameter
SW1
SW2
SW3
SS1
SS2
SS3
1
pH
8.11
8.64
8.42
7.98
8.64
8.15
2
TDS (mg/L)
914.4
1070.6
800.8
1054.1
1255.8
1094
3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
EC (g/cm) Salinity (ppt) Do (mg/L) BOD (mg/L) TA (mg/L) TH (mg/L) Ca2+ (mg/L) Mg2+ (mg/L) Na+ (mg/L) K+ (mg/L) HCO3- (mg/L) CO3- (mg/L) Cl- (mg/L) SO42 (mg/L) N.NO2- (mg/L) OPO4- (mg/L)
1451.4 ~1 4.6 65.3 141 174.8 83.5 91.3 120.5 54.7 136.4 4.6 321.5 72.8 6.4 11.4
1699.3 ~1 3.5 70.1 202 156.9 72.4 84.5 104.2 71.6 185.6 16.4 400.8 81.3 14.5 25.9
1271.1 ~1 3.1 61.2 162.8 148 68.9 79.1 93.4 55.4 151.2 11.6 247.8 60.5 8.9 14.6
1673.1 ~1 2.8 89.4 171.5 222.7 101.4 121.3 108.9 64.8 160.1 11.4 365.2 80.5 10.5 12.4
1993.3 ~1 1.8 105.7 224.8 276.4 124.8 151.6 129.5 70.5 203.4 21.4 402.6 84.7 18.9 29.8
1736.5 ~1 2.2 91.5 203.1 239.1 108.4 130.7 115.8 76.8 186.7 16.4 334.5 76.5 12.4 21.3
19
Oil & Grease(mg/L)
11.3
13.4
9.4
17.6
18.6
14.5
According to Dorn et al. (1998), hydrocarbon contains substances that are toxic to the flora and fauna found in the ecosystem. Diesel pollution is on the increase in Nigeria, as well as other developing countries 23. The trace metal parameters of petrol and diesel oil contaminated soil and water samples in mechanic workshop for the season post-monsoon was given in Table 3. The presence of heavy metals in the environment and specifically in soils, industrial and domestic urban wastes endagers living organisms. Once it gets into food chain, through plants, animals and water sources leads to biomagnification and bioaccumulation in living cells and tissues24-25. Table 3. Trace metal parameters in oil polluted area water and sediment samples in Tiruchirappalli, Tamil Nadu – Summer 2015 S. No.
Parameter
SW1
SW2
SW3
SS1
SS2
SS3
1
Cd
2.12
4.1
2.41
3.31
4.69
2.96
2
Cr
0.68
1.12
0.57
0.95
1.21
1.03
3
Cu
2.78
4.23
3.18
4.87
5.58
4.38
4
Fe
8.92
10.56
7.45
15.65
18.94
16.54
5
Ni
0.31
0.52
0.35
0.35
0.72
0.42
6
Pb
2.14
2.64
1.87
3.12
4.12
3.64
7
Zn
4.56
5.98
4.12
7.45
9.26
7.95
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Int. J. Life. Sci. Scienti. Res., VOL 2, ISSUE 2
Totally 31 isolates were isolated from different samples from three different sites namely oil contaminated sites from mechanic workshop. All the strains were used for screening of PHA production.
SCREENING FOR PHA PRODUCING BACTERIAL STRAINS Totally five isolates from site 1 water sample (SW1) namely Acinetobacter sp, Aeromonas sp, Aeromonas sp, Alcaligenes sp and Bacillus sp among the isolates only one strain Bacillus sp showed PHA accumulation. In site 1 sediment sample (SS1) five bacterial strains were isolated such as Bacillus sp, Bacillus sp, Enterobacter sp, Lactobacillus sp, Listeria sp. From site 2 water sample (SW3) five bacterial strains were isolated namely Paenibacillus sp and from site 2 sediment sample (SS2) five isolates were identified. In site 3 water sample (SW3) five bacterial strains were isolated namely Pasteurella sp and different types of Pseudomonas sp were isolated and from sediment sample (SS3), six isolates were isolated such as Serratia sp, Citrobacter sp, staphylococcus sp and different types of Vibrio sp. These bacterial strains were identified and confirmed by morphological and biochemical test with the help of nineth editions of Bergey’s manual of determinative bacteriology. The result of biochemical test was given on Table 4. Hence out of thiry one isolates one strain are screened for high PHA producers based on nile blue A staining (Fig. 1).
+ + +/-
+ + + + + + + + + + + + + + + + +/-
+ + + + + +/+ + + + + -
+/+/+/+/+ +/+/-
+/+ +/+ + + + + + + -
+ + + +/+/+ + +/+ + +
+ + + + + + + + + + -
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + -
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+/+/+ +/+/+/+/+/+/+/+ + + +/+ + + +
+ + + + + + + + -
Cocci/ rods
+ + + + + + +/+ + + + + + + + + + + + + + +
L-Phenyl alanine Gram Staining
Sporulation
+ + + + + + + + + + +
Motility
+ + + + + + + + + + + + + + + +/-
Esculin
+ + + + + + + + + + + + + + +/+
ONPG
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +/+
Gelatin
+ + + +/+ + + + + -
Coagulase
+ + -
Casein Hydrolysis
Ak Ak Ac Ac Ak Ak Ac Ac Ac Ac Ac Ac Ac Ac Ac Ak Ak Ak Ak Ak Ac Ac Ac Ac Ac Ac Ac Ac Ac Ac Ac
Nitrate
Urease
AK Ak Ac Ak Ak Ac Ac Ac Ac Ac Ak Ak Ak Ak Ak Ac Ak Ak Ak Ak Ak Ak Ak Ak Ak Ak Ac Ak Ak Ak Ak
Starch Hydrolysis Carbohydrate
Oxidase
+ + + + + + + + + + + + + + + + + + + + +
Catalase
Citrate
+ + + + + + + + +/+ + + + +
Gas
Voges Proskauer
+ + + + + + + +
H2S
Methyl Red
+ + + + + +/+
But
Indole
B1 B2 B3 B4 B5 B6 B7 B8 B9 B10 B11 B12 B13 B14 B15 B16 B17 B18 B19 B20 B21 B22 B23 B24 B25 B26 B27 B28 B29 B30 B31
TSI
Slant
Culture code
Table 4. Biochemical characterizations of isolated strains from oil polluted regions in Tiruchirappalli
Rods coccobacilli Rods Rods Rods Rods Rods Rods Rods coccobacilli Rods Rods Rods Rods Rods coccobacilli Rods Rods Rods Rods Rods Rods Rods Rods Rods Rods Rods Cocci coccobacilli Rods coccobacilli
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Int. J. Life. Sci. Scienti. Res., VOL 2, ISSUE 2
Fig 1. Nile blue A test for Bacillus spp.
Molecular Identification of Pure Isolate Using 16S rRNA The sequence of partial 16srRNA of this strain was compared against those available in the public database. The sequence is closely related to Bacillus sp (97% identity to 16srRNA sequence of similarity to strains). The nucleotide sequence and phylogeny based on these partial 16s rRNA sequences and related to bacterial strains are shown in Fig. 2 and Fig. 3. The
nucleotide sequence of
cgaaggcggc 721 tttttggtct gtaactgacg ctgaggcgcg aaagcgtggg gagcaaacag gattagatac 781 cctggtagtc cacgccgtaa acgatgagtg ctaagtgtta gagggtttcc gccctttagt 841 gctgcagcta acgcattaag cactccgcct ggggagtacg gtcgcaagac tgaaactcaa 901 aggaattgac gggggcccgc acaagcggtg gagcatgtgg tttaattcga agcaacgcga 961 agaaccttac caggtcttga catcctctga caactctaga gatagagcgt tccccttcgg 1021 gggacagagt gacaggtggt gcatggttgt cgtcagctcg tgtcgtgaga tgttgggtta 1081 agtcccgcaa cgagcgcaac ccttgatctt agttgccagc atttagttgg gcactctaag 1141 gtgactgccg gtgacaaacc ggaggaaggt ggggatgacg tcaaatcatc atgcccctta 1201 tgacctgggc tacacacgtg ctacaatgga tggtacaaag ggctgcaaga ccgcgaggtc 1261 aagccaatcc cataaaacca ttctcagttc ggattgtagg ctgcaactcg cctacatgaa 1321 gctggaatcg ctagtaatcg cggatcagca tgccgcggtg aatacgttcc cgggccttgt 1381 acacaccgcc cgtcacacca cgagagtttg taacacccga agtcggtgga gtaaccgtaa 1441 ggagctagcc gcctaaggtg ggacagatga ttggggtgaa gtcgtacggc taccccaaaa 1501 atgcccgcgg gagatgatcg tgatttcaag cggttctgga cactaaaacc ccctaccaga 1561 gaatgcttcg atacatcctc gccctcttcc gctcccagtc aagctccctt ctcctgttca 1621 gcctctcgct tgcatgtgtc gccgcacctc ctcgatgaaa cacgggcttta
16s rRNA of the strain Bacillus cereus determined in this study have been deposited the in Gen Bank database under accession number KU512626. ORIGIN 1 cgtaggatga cgctggcggc gtgcctaata catgcaagtc gagcgaactg attagaagct 61 tgcttctatg acgttagcgg cggacgggtg agtaacacgt gggcaacctg cctgtaagac 121 tgggataact tcgggaaacc gaagctaata ccggatagga tcttctcctt catgggagat 181 gattgaaaga tggtttcggc tatcacttac agatgggccc gcggtgcatt agctagttgg 241 tgaggtaacg gctcaccaag gcaacgatgc atagccgacc tgagagggtg atcggccaca 301 ctgggactga gacacggccc agactcctac gggaggcagc agtagggaat cttccgcaat 361 ggacgaaagt ctgacggagc aacgccgcgt gagtgatgaa ggctttcggg tcgtaaaact 421 ctgttgttag ggaagaacaa gtacgagagt aactgctcgt accttgacgg tacctaacca 481 gaaagccacg gctaactacg tgccagcagc cgcggtaata cgtaggtggc aagcgttatc 541 cggaattatt gggcgtaaag cgcgcgcagg cggtttctta agtctgatgt gaaagcccac 601 ggctcaaccg tggagggtca ttggaaactg gggaacttga gtgcagaaga gaaaagcgga 661 attccacgtg tagcggtgaa atgcgtagag atgtggagga acaccagtgg
CONCLUSION This study has led to the preliminary finding of bacterial spps. Bacillus cereusfrom oil contaminated mechanic workshop water sample capable of producing PHA. It was also observed that physicochemical and trace metal content of the site.
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Int. J. Life. Sci. Scienti. Res., VOL 2, ISSUE 2 [9] Vignesh S, Dahms HU, Emmanuel KV, Gokul MS,
ACKNOWLEDGEMENT One of authors (R. Rameshwari) is highly thankful to University Grants Commission (UGC), for financial support by receiving Minor Research Project (SERO/UGC, Hyderabad) No: MRP – 6112/15). Authors also thankful to Department of Civil Engineering, National Institute of Technolgy (NIT), Trichy, Tamilnadu, India for trace metal analysis.
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